Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 86257.52 
• Atom Count: 5986 
• Residue Count: 788 
• Unique protein chains: 1

2AY6

AROMATIC AMINO ACID AMINOTRANSFERASE WITH 3-INDOLEBUTYRIC ACID

• DOI: 10.2210/pdb2AY6/pdb

• Classification: AMINOTRANSFERASE
• Organism(s): Paracoccus denitrificans
• Expression System: Escherichia coli


• Deposited: 1998-08-06 Released: 1999-02-02 
• Deposition Author(s): Okamoto, A., Hirotsu, K., Kagamiyama, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.258 
• R-Value Work: 0.192 

Literature

The active site of Paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: flexibility and rigidity.

Okamoto, A., Ishii, S., Hirotsu, K., Kagamiyama, H.

(1999) Biochemistry 38: 1176-1184

• PubMed: 9930977 
• DOI: 10.1021/bi981921d
• Primary Citation of Related Structures:  
  2AY9, 2AY8, 2AY7, 2AY5, 2AY4, 2AY3, 2AY2, 2AY1


• PubMed Abstract: 
  

Paracoccus denitrificans aromatic amino acid aminotransferase (EC 2. 6.1.57; pdAroAT) binds with a series of aliphatic monocarboxylates attached to the bulky hydrophobic groups. To analyze the properties of the active site in this enzyme, we determined the tertiary structures of pdAroAT complexed with nine different inhibitors. Comparison of these active site structures showed that the active site of pdAroAT consists of two parts with contrary properties: rigidity and flexibility. The regions that interact with the carboxylates and methylene chains of the inhibitors gave essentially the same structures among these complexes, exhibiting the rigid property, which would involve fixing the substrate at the proper orientation for efficient catalysis. The region that interacts with the terminal hydrophobic groups of the inhibitors gave versatile structures according to the structures of the terminal groups, showing that this region is structurally flexible. This is mainly achieved by the conformational versatility of the side chains of Asp15, Lys16, Asn142, Arg292, and Ser296. These residues formed in the active site hydrogen bond networks, which were adaptable for the structures of the terminal hydrophobic groups of the inhibitors, with a small deformation or partial destruction according to the shapes and sizes of the inhibitors. These observations illustrate how the flexibility and rigidity in the active site can be used for the substrate binding and recognition.

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Related Citations: 

• Crystal Structures of Paracoccus Denitrificans Aromatic Amino Acid Aminotransferase: A Substrate Recognition Site Constructed by Rearrangement of Hydrogen Bond Network
  Okamoto, A.,Nakai, Y.,Hayashi, H.,Hirotsu, K.,Kagamiyama, H.
  (1998) J.Mol.Biol. 280: 443
• Paracoccus Denitrificans Aromatic Amino Acid Aminotransferase: A Model Enzyme for the Study of Dual Substrate Recognition Mechanism
  Oue, S.,Okamoto, A.,Nakai, Y.,Nakahira, M.,Shibatani, T.,Hayashi, H.,Kagamiyama, H.
  (1997) J.Biochem.(Tokyo) 121: 161




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Organizational Affiliation: 

Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka 569-8686, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
AROMATIC AMINO ACID AMINOTRANSFERASE	A, B	394	Paracoccus denitrificans	Mutation(s): 0  Gene Names: tyrB EC: 2.6.1.57
Find proteins for P95468 (Paracoccus denitrificans) Go to UniProtKB:  P95468

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PLP	A, B	PYRIDOXAL-5'-PHOSPHATE VITAMIN B6 Phosphate C8 H10 N O6 P NGVDGCNFYWLIFO-UHFFFAOYSA-N
3IB	B	3-INDOLEBUTYRIC ACID C12 H13 N O2 JTEDVYBZBROSJT-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
3IB	Kd: 780000 nM BINDINGMOAD
3IB	Kd: 780000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.2 Å
• R-Value Free: 0.258 
• R-Value Work: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 124.010	α = 90.00
b = 121.780	β = 90.00
c = 55.130	γ = 90.00

Software Package:

Software Name	Purpose
PROCESS	data reduction
PROCESS	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-08-06 
• Released Date: 1999-02-02 
• Deposition Author(s): Okamoto, A., Hirotsu, K., Kagamiyama, H.

Revision History 

• Version 1.0: 1999-02-02
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance
• Version 1.3: 2017-11-29
  Type: Derived calculations, Other